Writing a harmonic potential. In this section, we will write a simple pairwise potential, that is, a harmonic potential, between two atoms. A radially-symmetric harmonic potential tries to exert a force upon an atom pointed in the direction of the minimum energy location. The functional form of the harmonic potential, , is given by the following:. Writing a harmonic potential. In this section, we will write a simple pairwise potential, that is, a harmonic potential, between two atoms. A radially-symmetric harmonic potential tries to exert a force upon an atom pointed in the direction of the minimum energy location. The functional form of the harmonic potential, , is given by the following:. They are only enabled if LAMMPS was built with: those packages. See the "Making LAMMPS"_Section_start.html#start_3: section for more info. You can specify the accelerated styles explicitly in your input script: by including their suffix, or you can use the "-suffix command-line: switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can. Harmonic -surface-mapping-algorithm-in- LAMMPS . HSMA3D and HSMA2D (with planar dielectric interfaces) have been implemented into LAMMPS as a k-space module. This module is written via C++ and is paralleled via MPI + OpenMP. We recommend user install 'user-omp' package in Lammps. The lammps_open() function is used to initialize LAMMPS, passing in a list of strings as if they were command-line arguments when LAMMPS is run in stand-alone mode from the command line, and a MPI communicator for LAMMPS to run under. It returns a ptr to the LAMMPS object that is created, and which is used in subsequent library calls.. "/>. These pair styles can only be used via the pair keyword of the run_style respa command. They do not support the inner, middle, outer keywords. Restrictions The harmonic/cut pair style is only enabled if LAMMPS was built with the EXTRA-PAIR package. See the Build package page for more info. pair_coeff Default none. Writing a harmonic potential In this section, we will write a simple pairwise potential, that is, a harmonic potential, between two atoms. A radially-symmetric harmonic potential tries to exert a force upon an atom pointed in the direction of the minimum energy location. The functional form of the harmonic > potential, , is given by the following:.

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Lammps harmonic

# Polymer simulation with LAMMPS. # Dr. Mark A. Tschopp, 2010. # Variables variable fname index PE_cl100.txt variable simname index PE_cl100 # Initialization units real boundary f f f atom_style molecular log log.${simname}.txt read_data ${fname} # Dreiding potential information neighbor 0.4 bin neigh_modify every 10 one 10000 bond_style harmonic bond_coeff 1 350 1.53 angle_style harmonic. The State of the LAMMPS KOKKOS Package Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. dihedral_style.

Lammps harmonic

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    For further references, see the fix atc documentation and examples in the examples/USER/atc/ directory of the LAMMPS source code. For example, to compute a 2D spatial map of electrostatic potential in the xz plane: units real boundary p p p. atom_style full bond_style harmonic angle_style harmonic dihedral .... The degree of freedom is defined .... # Polymer simulation with LAMMPS. # Dr. Mark A. Tschopp, 2010. # Variables variable fname index PE_cl100.txt variable simname index PE_cl100 # Initialization units real boundary f f f atom_style molecular log log.${simname}.txt read_data ${fname} # Dreiding potential information neighbor 0.4 bin neigh_modify every 10 one 10000 bond_style harmonic bond_coeff 1 350 1.53 angle_style harmonic. The lammps_open() function is used to initialize LAMMPS, passing in a list of strings as if they were command-line arguments when LAMMPS is run in stand-alone mode from the command line, and a MPI communicator for LAMMPS to run under. It returns a ptr to the LAMMPS object that is created, and which is used in subsequent library calls.. "/>. LAMMPS mail list The LAMMPS mailing list was hosted since 2005 at SourceForge and was discontinued on June 30th 2022. In 2021, LAMMPS joined the Materials Science Community Discourse website as a forum for discussions about LAMMPS. See forum details here. This is now the main place for communication of the LAMMPS user and developer community.. Harmonic surface mapping Molecular dynamics Dielectric mismatch LAMMPS 1. Introduction Electrostatic interactions play a key role in nanoparticle self-assembly processes [1], [2], and are also ubiquitous in biomolecular systems, such as DNA aggregation [3] and polyelectrolyte complexation [4], [5], [6]. "/>. About Lammps Theory . In such case, a random resistor network can be considered as a two-dimensional graph and the effective resistance can be modelled in terms of graph measures. ... and then how the geometry of metric spaces of curvature bounded above influences the behavior of harmonic maps. Yes, i am using LAMMPS's 30 Sep 2016 version.. The LAMMPS convention is that the trans position = 180 degrees, while in some force fields trans = 0 degrees. Some force fields reverse the sign convention on d. Some force fields let n be positive or negative which corresponds to d = 1 or d = − 1 for the harmonic style.. "/>.

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    2022. 6. 22. · Accelerator Variants: harmonic/intel, harmonic/kk, harmonic/omp. ... but LAMMPS converts it to radians internally; hence \(K\) is effectively energy per radian^2. Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. Apr 15, 2020 · This tutorial shows how to generate a Sigma5 (310) symmetric tilt grain boundary in aluminum. LAMMPS Beginner Help 6. This tutorial calculates stresses for the fracture of an iron symmetric tilt grain boundary. LAMMPS Beginner Help 8. This tutorial calculates the stacking fault energy curve for FCC in LAMMPS..

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    Check you data file, and find out how many types of impropers you have. For each type you should have a corresponding coeff line in the input script. As for LAMMPS documentation: https://docs.

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    Harmonic surface mapping Molecular dynamics Dielectric mismatch LAMMPS 1. Introduction Electrostatic interactions play a key role in nanoparticle self-assembly processes [1], [2], and are also ubiquitous in biomolecular systems, such as DNA aggregation [3] and polyelectrolyte complexation [4], [5], [6]. "/>. A radially-symmetric harmonic potential tries to exert a force upon an atom pointed in the direction of the minimum energy location. The functional form of the harmonic potential, , is given by the following:. classmethod from_phonopy (path = '. io/phonopy/)LAMMPS python interface (https://lammps. Affitto case, appartamenti, uffici e negozi. Apr 15, 2020 · Abstract. In this tutorial Molecular dynamics simulation in LAMMPS is used to show what happens to a polymer chain at a certain temperature after some time. Chain's movement is caused by a molecular forces between atoms in the chain and by temperature of the chain. This factors are modeled in LAMMPS in order to show the behavior of this polymer .... LAMMPS - An Object Oriented Scientific Application. Workshop on Computer Programming and Advanced Tools for Scientific Research Work LAMMPS is a Collaborative Project A few lead developers and many significant contributors: ... harmonic constraint forces, collective variables. A brief survey of the LAMMPS > particle simulation code: introduction, case studies, and future. Apr 15, 2020 · This tutorial shows how to generate a Sigma5 (310) symmetric tilt grain boundary in aluminum. LAMMPS Beginner Help 6. This tutorial calculates stresses for the fracture of an iron symmetric tilt grain boundary. LAMMPS Beginner Help 8. This tutorial calculates the stacking fault energy curve for FCC in LAMMPS.. improper_style harmonic improper_coeff 1 100.0 0 Description The harmonic improper style uses the potential E = K ( χ − χ 0) 2 where χ is the improper angle, χ 0 is its equilibrium value, and K is a prefactor. Note that the usual 1/2 factor is included in K. The supplied zip file contains a pdf Abstract. 1 Harmonic excitation of an undamped SDOF system mu&+ku =p o cosΩt (4. Abbasi May 30, 2012 Compiled on May 20, 2020 at 9:23pm Contents 1 download examples source code 1 2 description 1 3 Simulation 3 4 Using ode45 with piecewise function 6 5 Listing of source code 6 1 download examples source code 1.

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    9/13) Significant features added to LAMMPS in the third quarter of 2013 include pair nb3b/harmonic, allow poly-disperse granular systems to have widely varying neighbors/particle, atomfile-style variables, fix property/atom to add new user-defined attributes to atoms, fix gld, compute basal/atom, pair tersoff/mod, pair peri/ves, new.

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    Check you data file, and find out how many types of impropers you have. For each type you should have a corresponding coeff line in the input script. As for LAMMPS documentation: https://docs. They are only enabled if LAMMPS was built with those packages. See the Build package doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.. 2022. 5. 24. · Quasi-harmonic approximation: Thermal expansion, heat capacity at constant pressure (Cp) Interfaces to calculators: VASP, VASP DFPT, ABINIT, Quantu ESPRESSO, SIESTA, Elk, WIEN2k, CRYSTAL, DFTB+, TURBOMOLE, CP2K, FHI-aims, CASTEP, Fleur, LAMMPS (external) Phonopy API for Python. A presentation in pdf for introduction to phonopy is downloaded here. May 07, 2019 · Proper dihedral potential: harmonic, Fourier and Ryckaert–Bellemans. Improper dihedral potential: harmonic. It is worth noticing that the harmonic constants in LAMMPS format (k LAMMPS) already include the usual 1/2 factor; thus, both bond and angle coefficients from GROMACS (k GROMACS) are converted as:. May 07, 2019 · Proper dihedral potential: harmonic, Fourier and Ryckaert–Bellemans. Improper dihedral potential: harmonic. It is worth noticing that the harmonic constants in LAMMPS format (k LAMMPS) already include the usual 1/2 factor; thus, both bond and angle coefficients from GROMACS (k GROMACS) are converted as:. It returns a ptr to the LAMMPS object that is created, and which is used in subsequent library calls.. The harmonic improper style uses the potential ... X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2. Jul 01, 2022 · The HSMA package is designed for efficient and accurate modeling of electrostatic interactions in 3D and 2D periodic systems with dielectric effects at O ( N) cost. The implementation is hybrid MPI and OpenMP parallelized and compatible with existing LAMMPS functionalities. The vectorization technique following AVX512 instructions is adopted .... Public development project of the LAMMPS MD software package - lammps/dihedral_harmonic.h at master · lammps/lammps. The LAMMPS convention is that the trans position = 180 degrees, while in some force fields trans = 0 degrees. Some force fields reverse the sign convention on d. Some force fields let n be positive or negative which corresponds to d = 1 or d = − 1 for the harmonic style. for example, if these are on the desktop, type 'cd h:/desktop' to change to the desktop.. (9/13) significant features added to lammps in the third quarter of 2013 include pair nb3b/harmonic, allow poly-disperse granular systems to have widely varying neighbors/particle, atomfile-style variables, fix property/atom to add new user-defined. LAMMPS Tutorial. Published in Technische Universität Darmstadt, Chemistry Department, 2019. LAMMPS Introduction What is LAMMPS? It is an acronym Large-scale Atomic/Molecular Massively Parallel Simulator; It is a classical molecular dynamics code with a focus on materials modeling; Open source, portable C++;. Dec 04, 2020 · folder_open LAMMPS Inputs. This is a LAMMPS input to study deformation mechanisms during uniaxial tensile deformation of an amorphous polyethylene polymer. The stress-strain behavior comprised elastic, yield, strain softening and strain hardening regions that were qualitatively in agreement with previous simulations and experimental results..

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    lammps力场大体分为两种情况:. ... . 2 DRDC-RDDC-2016-R152. A simple harmonic oscillator is an oscillator that is neither driven nor damped 9 m occurs when t = 0 + AMDAVX = AMD 64-bit x86 CPUs Sekarang kita persiapkan tools dan materials nya terlebih dahulu,. Read Dump Lammps . chicago gang map google; vitacci scooters; apwh unit 1 practice test; yakitori boy yelp; hidden hills ca celebrity homes; zanussi gas cooker parts; tire cupping; celecoxib covid 2021; p2500 p2502 mercedes; 1988 oldsmobile parts; 1911 optic cut slide; mitsubishi fuso crank no start; fiberfab.

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    which is really, really bad. you cannot expect reasonable results, when part of your interactions is missing. > > when I run my code, I face this error: > > > ERROR: Incorrect sign arg for dihedral coefficients (../dihedral_harmonic.cpp:290). > > I changed the sign of 1 in dihedrals but it does not work. I don not know what the problem is. They are only enabled if LAMMPS was built with those packages. See the Build package doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.. 2021. 5. 5. · Harmonic impropers: I am going to compare manually computed energies with LAMMPS and GROMACS. parmed preserves the harmonic improper order when reading/writing gmx files. For example, if the topology has an improper with the atoms listed in order 1 4 3 2 , then the atom1.idx , atom2.idx , etc, in parmed have the same order. LAMMPS - An Object Oriented Scientific Application. Workshop on Computer Programming and Advanced Tools for Scientific Research Work LAMMPS is a Collaborative Project A few lead developers and many significant contributors: ...harmonic constraint forces, collective variables. A simple harmonic oscillator is an oscillator that is neither driven nor damped 9 m occurs when t. Harmonic-surface-mapping-algorithm-in-LAMMPS HSMA3D and HSMA2D (with planar dielectric interfaces) have been implemented into LAMMPS as a k-space module. This module is written via C++ and is paralleled via MPI + OpenMP. We recommend user install 'user-omp' package in Lammps. Fewer MPIs and more OpenMPs are the most efficient choice.. Jun 01, 2022 · Circles are for single point particles (N = 1), squares are for 4-point (N r = 4) and triangles for 6-point (N r = 6) composite particles, both with nodes within a shell of radius 0.204Δx and with fixed relative distances (implemented using the standard LAMMPS rigid fix), and diamonds for 4-point composite particles (N b = 4) with harmonic..... Search: Vasp Dipole Moment. I now can calculate dipole moment matrix, also the strength of dipole moment accurately, but I can not figure out the direction of dipole moment Write density in gOpenMol cube format 11 The dipole center was set at the center of the unit cell Methanol is the primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and. 2013. 2. 13. · While visualizing > the > > trajectories; in case (1), all beads are reasonably flushed away, since > > there is no spring at all. In case (2), I assumed it would be the same, > > since the bonds are weak as nothing, and all beads should be flushed away > > with the breaking of bonds. However, the beads in a chain are squeezed to > > small. May 05, 2016 · From bond_harmonic potential, through analogy, I determine what parameters I need to provide through the input file, how to read the parameters, initialize any necessary memory address, and how to calculate the force due to the potential. From my experience, this is the most effective way of learning or modifying lammps... Jun 01, 2022 · Circles are for single point particles (N = 1), squares are for 4-point (N r = 4) and triangles for 6-point (N r = 6) composite particles, both with nodes within a shell of radius 0.204Δx and with fixed relative distances (implemented using the standard LAMMPS rigid fix), and diamonds for 4-point composite particles (N b = 4) with harmonic..... Description. Set the formula(s) LAMMPS uses to compute bond interactions between pairs of atoms. In LAMMPS , a bond differs from a pairwise interaction, which are set via the pair_style command. Bonds are defined between specified pairs of atoms and remain in force for the duration of the simulation (unless the bond breaks which is possible in some bond potentials). In a LAMMPS input script, the corresponding syntax for implementing a wall is as follows: ... which is the type of potential between the wall and an atom, such as Lennard-Jones (LJ), Morse, and Harmonic; FACE, which is the direction that the wall is facing in, and can be one of ;.In this video, I show how to setup the geometry for a two element simulation in LAMMPS, and how to. They are only enabled if LAMMPS was built with those packages. See the Build package doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.. It returns a ptr to the LAMMPS object that is created, and which is used in subsequent library calls.. The harmonic improper style uses the potential ... X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2. improper_style harmonic improper_coeff 1 100.0 0 Description. The harmonic improper style uses the potential. where X is the improper angle, X0 is its equilibrium value, and K is a prefactor. ... X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2. Styles with a gpu, intel,. wix repeater api cracked bushings car; 2 bedroom house for rent cheap all bills paid. Harmonic surface mapping Molecular dynamics Dielectric mismatch LAMMPS 1. Introduction Electrostatic interactions play a key role in nanoparticle self-assembly processes [1], [2], and are also ubiquitous in biomolecular systems, such as DNA aggregation [3] and polyelectrolyte complexation [4], [5], [6]. "/>. Overview ¶. Define a bonding potential energy function corresponding to a harmonic bond style. U i j = 1 2 k ( r − r 0) 2, where k, r 0 are parameters that must be set to define the interaction between atoms i, j . Bonds and types can be defined directly within the python input script, read from a LAMMPS data file (using the LAMMPS reader. They are only enabled if LAMMPS was built with: those packages. See the "Making LAMMPS"_Section_start.html#start_3: section for more info. You can specify the accelerated styles explicitly in your input script: by including their suffix, or you can use the "-suffix command-line: switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can. 2013. 2. 13. · While visualizing > the > > trajectories; in case (1), all beads are reasonably flushed away, since > > there is no spring at all. In case (2), I assumed it would be the same, > > since the bonds are weak as nothing, and all beads should be flushed away > > with the breaking of bonds. However, the beads in a chain are squeezed to > > small. LAMMPS - An Object Oriented Scientific Application. Workshop on Computer Programming and Advanced Tools for Scientific Research Work LAMMPS is a Collaborative Project A few lead developers and many significant contributors: ...harmonic constraint forces, collective variables. A simple harmonic oscillator is an oscillator that is neither driven nor damped 9 m occurs when t. Harmonic-surface-mapping-algorithm-in-LAMMPS. HSMA3D and HSMA2D (with planar dielectric interfaces) have been implemented into LAMMPS as a k-space module. This module is written via C++ and is paralleled via MPI + OpenMP. We recommend user install 'user-omp' package in Lammps. Fewer MPIs and more OpenMPs are the most efficient choice.. The supplied zip file contains a pdf Abstract. 1 Harmonic excitation of an undamped SDOF system mu&+ku =p o cosΩt (4. Abbasi May 30, 2012 Compiled on May 20, 2020 at 9:23pm Contents 1 download examples source code 1 2 description 1 3 Simulation 3 4 Using ode45 with piecewise function 6 5 Listing of source code 6 1 download examples source code 1.

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    They are only enabled if LAMMPS was built with: those packages. See the "Making LAMMPS"_Section_start.html#start_3: section for more info. You can specify the accelerated styles explicitly in your input script: by including their suffix, or you can use the "-suffix command-line: switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can. A radially-symmetric harmonic potential tries to exert a force upon an atom pointed in the direction of the minimum energy location. The functional form of the harmonic potential, , is given by the following:. classmethod from_phonopy (path = '. io/phonopy/)LAMMPS python interface (https://lammps. Affitto case, appartamenti, uffici e negozi. Harmonic -surface-mapping-algorithm-in- LAMMPS . HSMA3D and HSMA2D (with planar dielectric interfaces) have been implemented into LAMMPS as a k-space module. This module is written via C++ and is paralleled via MPI + OpenMP. We recommend user install 'user-omp' package in Lammps. 2022. 5. 24. · Quasi-harmonic approximation: Thermal expansion, heat capacity at constant pressure (Cp) Interfaces to calculators: VASP, VASP DFPT, ABINIT, Quantu ESPRESSO, SIESTA, Elk, WIEN2k, CRYSTAL, DFTB+, TURBOMOLE, CP2K, FHI-aims, CASTEP, Fleur, LAMMPS (external) Phonopy API for Python. A presentation in pdf for introduction to phonopy is downloaded here. 2019. 6. 5. · The harmonic improper style uses the potential. where X is the improper angle, ... X0 is specified in degrees, but LAMMPS converts it to radians internally; hence the units of K are in energy/radian^2. Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix.

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    Overview ¶. Define a bonding potential energy function corresponding to a harmonic bond style. U i j = 1 2 k ( r − r 0) 2, where k, r 0 are parameters that must be set to define the interaction between atoms i, j . Bonds and types can be defined directly within the python input script, read from a LAMMPS data file (using the LAMMPS reader. Note that the '.lammps' extension has no importance. Copy the following lines into input.01.lammps: # Initialisation units real atom_style full bond_style harmonic angle_style harmonic pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 12.0 kspace_style pppm/tip4p 1.0e-4. Explanations: There are many differences with respect to tutorial 01. With the. lammps力场大体分为两种情况:. ... . 2 DRDC-RDDC-2016-R152. A simple harmonic oscillator is an oscillator that is neither driven nor damped 9 m occurs when t = 0 + AMDAVX = AMD 64-bit x86 CPUs Sekarang kita persiapkan tools dan materials nya terlebih dahulu,. Writing a harmonic potential In this section, we will write a simple pairwise potential, that is, a harmonic potential, between two atoms. A radially-symmetric harmonic potential tries to exert a force upon an atom pointed in the direction of the minimum energy location. The functional form of the harmonic > potential, , is given by the following:. LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator Simulaciones Moleculares de grano grueso. Diferentes tipos de “ átomos de grano grueso”. Moléculas puntuales, esféricas.

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where \(\theta_0\) is the equilibrium value of the angle, and \(K\) is a prefactor. Note that the usual 1/2 factor is included in \(K\).. The following coefficients must be defined for each angle type via the angle_coeff command as in the example above, or in the data file or restart files read by the read_data or read_restart commands:
LAMMPS Tutorial. Published in Technische Universität Darmstadt, Chemistry Department, 2019. LAMMPS Introduction What is LAMMPS? It is an acronym Large-scale Atomic/Molecular Massively Parallel Simulator; It is a classical molecular dynamics code with a focus on materials modeling; Open source, portable C++;
Dec 06, 2020 · # Polymer simulation with LAMMPS. # Dr. Mark A. Tschopp, 2010. # Variables variable fname index PE_cl100.txt variable simname index PE_cl100 # Initialization units real boundary f f f atom_style molecular log log.${simname}.txt read_data ${fname} # Dreiding potential information neighbor 0.4 bin neigh_modify every 10 one 10000 bond_style harmonic bond_coeff 1 350 1.53 angle_style harmonic ...
Writing a harmonic potential In this section, we will write a simple pairwise potential, that is, a harmonic potential, between two atoms. A radially-symmetric harmonic potential tries to exert a force upon an atom pointed in the direction of the minimum energy location. The functional form of the harmonic > potential, , is given by the following:.
# Polymer simulation with LAMMPS. # Dr. Mark A. Tschopp, 2010. # Variables variable fname index PE_cl100.txt variable simname index PE_cl100 # Initialization units real boundary f f f atom_style molecular log log.${simname}.txt read_data ${fname} # Dreiding potential information neighbor 0.4 bin neigh_modify every 10 one 10000 bond_style harmonic bond_coeff 1 350 1.53 angle_style harmonic ...